crossing96/oncoscreening huggingface dataset:
Quantitative functional profiling of ERCC2 mutations deciphers cisplatin sensitivity in bladder cancer.	Tumor gene alterations can serve as predictive biomarkers for therapy response. The nucleotide excision repair (NER) helicase ERCC2 carries heterozygous missense mutations in approximately 10% of bladder tumors, and these may predict sensitivity to cisplatin treatment. To explore the clinical actionability of ERCC2 mutations, we assembled a multinational cohort of 2,012 individuals with bladder cancer and applied the highly quantitative CRISPR-Select assay to functionally profile recurrent ERCC2 mutations. We also developed a single-allele editing version of CRISPR-Select to assess heterozygous missense variants in their native context. From the cohort, 506 ERCC2 mutations were identified, with 93% being heterozygous missense variants. CRISPR-Select pinpointed deleterious, cisplatin-sensitizing mutations, particularly within the conserved helicase domains. Importantly, single-allele editing revealed that heterozygous helicase-domain mutations markedly increased cisplatin sensitivity. Integration with clinical data confirmed that these mutations were associated with improved response to platinum-based neoadjuvant chemotherapy. Comparison with computational algorithms showed substantial discrepancies, highlighting the importance of precision functional assays for interpreting mutation effects in clinically relevant contexts. Our results demonstrate that CRISPR-Select provides a robust platform to advance biomarker-driven therapy in bladder cancer and supports its potential integration into precision oncology workflows.	bladder
Enfortumab vedotin-induced bullous dermatitis.	Enfortumab vedotin is a first-in-class antibody-drug conjugate used in the treatment of locally advanced or metastatic urothelial carcinoma. A range of cutaneous adverse events has been reported with enfortumab vedotin use. Nectin-4, a transmembrane protein overexpressed by urothelial carcinoma cells, is the intended target of enfortumab vedotin. However, as nectin-4 is also expressed by epidermal keratinocytes, sweat glands, and hair follicles, it is believed that cutaneous toxicity is mediated though off-target delivery of enfortumab vedotin. We present a patient with metastatic urothelial carcinoma who developed a grade 3 bullous dermatitis after his second treatment cycle of enfortumab vedotin and pembrolizumab therapy. Histopathologic findings showed intraepidermal blisters with prominent dyskeratotic and necrotic keratinocytes. Temporary withholding of enfortumab vedotin and pembrolizumab and treatment with potent topical corticosteroids led to significant improvement and enfortumab vedotin (with pembrolizumab) was resumed at a reduced dosage of enfortumab vedotin without recurrence. We present this case to highlight the clinical manifestations, histopathologic findings, and management of enfortumab vedotin-induced cutaneous toxicity.	bladder
Emotional stress: a prominent factor positively related to the onset and recurrence of bladder cancer as revealed by NHANES and a Chinese database.	BACKGROUND AND OBJECTIVE: Bladder cancer and emotional stress are both common physiologic problems, with few published studies and a lack of studies with large samples discussing their association. The aim of this study was to investigate the association between bladder cancer and emotional stress. RESEARCH METHODS: We used data from the U.S. National Health and Nutrition Examination Survey (NHANES) database for the period 2005 to 2020 and the Bladder Cancer Database from Shanghai Tenth People's Hospital of Tongji University. The above two databases were used for two independent cross-sectional studies, respectively. We adopted the method of multivariate logistic regression to analyze the relationship between the occurrence of bladder cancer and depression, as well as the relationship between the recurrence of bladder cancer and emotional stress. RESULTS: Based on the NHANES database, a total of 23,801 participants were enrolled in our study, including 100 participants diagnosed with bladder cancer and 23,701 participants not diagnosed with bladder cancer. After adjustment for covariates, there was a significant positive association between bladder cancer and mild depression (OR: 2.43, 95% CI: 1.41, 4.00). There was a significant positive association between recurrence of bladder cancer and general depression (OR: 2.16, 95% CI: 1.20, 3.88) among 303 bladder cancer patients in the Chinese database. CONCLUSION: This study reveals a strong association between bladder cancer and emotional stress, with patients with bladder cancer having a significant risk of depression and elevated emotional stress potentially associated with bladder cancer recurrence.	bladder
FGFR3 alteration sites and response rate to FGFR inhibitors in urothelial carcinoma.	Dysregulation of fibroblast growth factor receptor (FGFR) signaling contributes to tumorigenesis and FGFRs have been clinically approved as treatment targets for FGFR inhibitor (FGFRi) in urothelial carcinoma (UC). The present study aimed to explore the correlations between different FGFR3 alteration sites and response to FGFRi. We involved a total of 1045 FGF/FGFR-altered UC patients treated with FGFRi, among whom 54.93 % carried FGFR3 mutations and 15.22 % carried FGFR3 fusions. Erdafitinib (47.37 %) was the most frequently used FGFRi drug in clinical studies. The objective response rate was 31.29 % in all participants. Higher frequencies of FGFR3-TACC3 fusion were positively correlated with elevated treatment response rates, particularly in complete response (coefficient=0.762, P = 0.028) and disease control (coefficient=0.786, P = 0.036), whereas FGFR3 S249C mutation showed a negative correlation with response. Similar results were identified in subgroup analyses. In conclusion, UC patients with FGFR3 fusions, especially FGFR3-TACC3 fusions, may benefit more from FGFRi than those with FGFR3 mutations, which highlighted the importance of FGFR3 alteration site test in determining the efficacy of FGFRi-based therapy and enhanced the patient benefit for FGF/FGFR-altered UC. Future studies with larger sample size and individual patient data are needed to confirm these findings and explore the underlying mechanisms of the differential response to FGFRi.	bladder
Guiding first-line treatment decisions in advanced urothelial carcinoma: a global survey.	BACKGROUND: Enfortumab vedotin combined with pembrolizumab (EV-P) has become the new standard first-line therapy for patients with advanced urothelial carcinoma (aUC), based on its superior efficacy over platinum-based chemotherapy. As this regimen is increasingly adopted in routine care, treatment decisions may often occur in sites without dedicated genitourinary oncology expertise. This global survey aimed to explore how physicians perceive clinical factors that may influence the safe and effective use of EV-P in daily practice. MATERIAL AND METHODS: A panel of international physicians with experience in treating patients with genitourinary cancers developed a 17-question survey addressing practice settings, experience in managing aUC, and clinical considerations relevant to the use of EV-P. The participants were recruited through a network-based convenience sampling method. The responses were descriptively analyzed. RESULTS: A total of 201 genitourinary physicians from 32 countries completed the questionnaire. The most frequently cited potential absolute contraindications were sensory or motor neuropathy grade ≥2 (64.2%), ECOG-PS ≥3 (59.2%), and non-urothelial component >50% of the tissue sample (59.2%). Other notable concerns included severe corneal/retinal abnormalities, HbA1c >11%, severe skin comorbidities, liver impairment grade ≥2, and dialysis dependence. CONCLUSIONS AND RELEVANCE: This survey provides practical insights into real-world physician perspectives on patient selection for EV-P. The findings highlight the need for guidance to support personalized risk assessment, facilitate early identification of patients who may require enhanced monitoring, and optimize safe integration of EV-P into clinical practice.	bladder
Urinary biomarkers for immunotherapy response in urothelial carcinoma: current status and future outlook.	INTRODUCTION: Immunotherapy treatments, such as intravesical Bacillus Calmette-Guérin (BCG) for non-muscle invasive bladder cancer (NMIBC) and systemic immune checkpoint inhibitors (ICIs) for all stages are central to the management of urothelial carcinoma (UC). Biomarkers that are prognostic or predictive and that help in monitoring these therapies are needed to guide and improve efficacy and tolerability. In this review, we evaluated the current landscape of urinary biomarkers for predicting response to immunotherapy (BCG and ICIs) in UC patients and their potential to guide personalized treatment strategies. AREAS COVERED: This narrative review summarizes current evidence on urinary biomarkers for predicting responses to BCG and ICIs therapies in UC, based on a comprehensive search of PubMed literature. EXPERT OPINION: Urinary biomarkers show significant potential for transforming UC immunotherapy by facilitating personalized treatment. Despite promising initial data for various analytes, large-scale validation and standardization must be addressed. We still need better, faster, easier, cheaper, reliable and valid urine-based biomarkers. Future research should focus on multiplex panels to enhance patient stratification and improve therapeutic outcomes and follow-up.	bladder
Modulating the PPARγ pathway upregulates NECTIN4 and enhances chimeric antigen receptor (CAR) T cell therapy in bladder cancer.	With the approval of the antibody-drug conjugate enfortumab vedotin (EV), NECTIN4 has emerged as a bona fide therapeutic target in urothelial carcinoma (UC). Here, we report the development of a NECTIN4-directed chimeric antigen receptor (CAR) T cell, which exhibits reactivity across cells expressing a range of endogenous NECTIN4, with enhanced activity in high expressors. We demonstrate that the PPARγ pathway, critical for luminal differentiation, transcriptionally controls NECTIN4, and that the PPARγ agonist rosiglitazone primes and augments NECTIN4 expression, thereby increasing sensitivity to NECTIN4-CAR T cell-mediated killing. NECTIN4-CAR T cells have potent anti-tumor activity even against EV resistant cells, which largely retain NECTIN4 expression, including in a post-EV biopsy cohort. Our results elucidate a therapeutically actionable mechanism that UC cells use to control NECTIN4 expression and suggest therapeutic approaches that leverage PPARγ agonists for rational combinations with NECTIN4-targeting agents in UC, as well as future potential treatment options for EV-refractory patients.	bladder
Urine cf-nucleosomes: A non-invasive window into human physiology and disease.	Urine contains fragments of cell-free DNA (cfDNA) that offer molecular insights into processes within the urinary system and the body. It remains unclear whether these fragments exist as chromatin and retain chromatin modifications from their cells of origin. Here, we employ cell-free chromatin immunoprecipitation followed by sequencing (cfChIP-seq) on human urine to address this issue. We show that cf-nucleosomes can be captured from urine and preserve histone modifications associated with gene activation and repression. Analysis in healthy individuals reveals distinct tissue contributions to urine cf-nucleosomes, including a kidney-derived population not detected in matched exfoliated cells or plasma. This suggests that kidney filtration largely excludes plasma cf-nucleosomes. In patients with bladder cancer, urine cf-nucleosomes reflect tumor-associated transcriptional programs and immune responses. These findings highlight the utility of urine cf-nucleosomes as accessible, non-invasive biomarkers for studying renal physiology and monitoring urinary pathologies.	bladder
Low-grade non-muscle-invasive bladder cancer: molecular landscape, treatment strategies and emerging therapies.	Low-grade non-muscle invasive bladder cancer is a specific category of bladder cancer with a favourable prognosis; however, its management presents several challenges. The risk of stage progression is very low, but approximately half of patients will experience recurrence within the first 5 years after diagnosis. This high propensity for recurrence, coupled with the threat of progression, mandates ongoing surveillance. However, the optimal frequency and duration of follow-up monitoring remain undefined. Current management strategies for low-grade non-muscle invasive bladder cancer rely heavily on routine office cystoscopy, with few advances in diagnostic and treatment options over the past 25 years. Our basic understanding of disease biology has substantially advanced. However, at present, considerable variations in clinical practice exist, with implications for increased financial and treatment burden for patients and health care systems. Molecular signatures and biomarker discoveries are crucial to understand disease behaviour and inform novel treatment strategies. Emerging therapies, such as advanced drug-delivery systems, immunomodulatory agents and targeted therapies, offer the potential to improve patient outcomes, streamline management and reduce the need for surveillance cystoscopies. Actionable avenues for future research in the field include prospective validation of novel biomarkers and therapies with the ultimate aim of optimizing patient care and reducing health care costs.	bladder
YTHDC2 suppresses bladder cancer by inhibiting SOX2-mediated tumor plasticity.	Pluripotent cancer stem cells play a pivotal role in inducing phenotypic plasticity across various cancer types, including bladder cancer. This plasticity, crucial for cancer progression, is largely regulated by epigenetic modifications including N6-methyladenosine (m(6)A) in RNAs. However, the role of the m(6)A reader protein YTHDC2 in this process remains poorly understood. In this study, we uncovered that the depletion of YTHDC2 significantly increased the pool of bladder cancer stem cells (BCSCs), resulting in a phenotypic shift towards a more invasive subtype of bladder cancer. This shift was characterized by enhanced proliferation, migration, invasion, and self-renewal capabilities of cancer cells, highlighting YTHDC2's function as a tumor suppressor. Mechanistically, YTHDC2 recognized and bound to m(6)A-modified SOX2 mRNA, resulting in translational inhibition of SOX2. In conclusion, our study identifies YTHDC2 as a tumor suppressor in bladder cancer through inhibiting SOX2-mediated cell pluripotency and underscores the therapeutic potential of targeting the YTHDC2-SOX2 axis in bladder cancer.	bladder
Lactate-driven lactylation of HNRNPA1 orchestrates PKM2 splicing and glycolytic reprogramming in bladder cancer.	BACKGROUND: Lactylation, a recently identified post-translational modification derived from lactate, has emerged as a regulator of tumor metabolism. However, its functional relevance and molecular targets in bladder cancer (BLCA) remain unclear. METHODS: We performed immunohistochemistry on patient tissues, global lactylation proteomics using LC-MS/MS, and in vitro and in vivo functional assays. Gene editing via CRISPR/Cas9, overexpression systems, and pharmacological interventions were employed to study P300-mediated HNRNPA1-K350 lactylation in driving BLCA cell aggression. Metabolomics and glycolytic flux assays were used to assess the metabolic consequences of HNRNPA1 lactylation. Molecular characterization was validated through gene expression and splicing analyses. Small-molecule drug screening was conducted via molecular docking to identify potential inhibitors targeting HNRNPA1. RESULTS: Protein lactylation levels were significantly elevated in BLCA tissues, correlating with poor prognosis. HNRNPA1 was identified as a central lactylation target. Glycolysis-induced lactate production promoted P300-mediated lactylation of HNRNPA1 at lysine 350, which facilitated PKM pre-mRNA splicing toward the PKM2 isoform, enhancing glycolytic flux and supporting tumor growth. Inhibition of glycolysis or LDHA knockdown reduced HNRNPA1 lactylation, suppressed PKM2 expression, and impaired BLCA cell proliferation, migration, and invasion. Metabolomic profiling linked HNRNPA1-K350 lactylation with increased aerobic glycolysis in BLCA cells. A small-molecule inhibitor, identified through molecular docking, attenuated cell proliferation by binding to HNRNPA1 and suppressing PKM2 expression. CONCLUSIONS: This study reveals a lactate-driven mechanism coupling alternative splicing to metabolic reprogramming via HNRNPA1 lactylation, identifying HNRNPA1-K350 lactylation as a key driver of glycolysis-dependent tumor progression. A therapeutic approach targeting HNRNPA1 in BLCA is proposed.	bladder
Efficacy and Safety of BL-B01D1 in Patients With Locally Advanced or Metastatic Urothelial Carcinoma: A Phase II Clinical Trial.	PURPOSE: To evaluate the efficacy and safety of BL-B01D1, a potential first-in-class epidermal growth factor receptor (EGFR)-human EGFR 3 bispecific antibody-drug conjugated (ADC) with Ed-04, in patients with locally advanced or metastatic urothelial carcinoma (la/mUC) refractory to standard or regular therapies. METHODS: BL-B01D1-201 is a multicenter, single-arm, phase II study of BL-B01D1 in patients with la/mUC who have progressed on systemic therapy. Patients received BL-B01D1 at a dose of 2.2, 2.5, or 2.75 mg/kg intravenously over approximately 60 minutes on days 1 and 8 once every 3 weeks. The primary end point was objective response rate (ORR). Secondary end points included progression-free survival (PFS), disease control rate (DCR), duration of response (DOR), and safety. RESULTS: A total of 41 patients were enrolled, 34 in 2.2 mg/kg, four in 2.5 mg/kg, and three in the 2.75 mg/kg group. In the 2.2 mg/kg group, the confirmed ORR was 44.1% (95% CI, 27.2 to 62.1) and the DCR was 88.2% (95% CI, 72.5 to 96.7). Among 15 patients who had received only one previous line of chemotherapy (either platinum-based or ADCs), the confirmed ORR achieved 80% (95% CI, 51.9 to 95.7). With a median follow-up of 10.2 months, the median PFS was 7.3 months (95% CI, 5.5 to 9.8) and the median DOR was 11.3 months (95% CI, 4.3 to not reached). The most common treatment-related adverse events (all grade/≥grade 3) were anemia (88.2%/38.2%), leukopenia (76.5%/38.2%), neutropenia (64.7%/41.2%), thrombocytopenia (64.7%/32.4%), appetite decrease (52.9%/2.9%), and nausea (52.9%/2.9%). CONCLUSION: BL-B01D1 showed promising preliminary efficacy and a favorable safety profile at 2.2 mg/kg in patients with la/mUC who had progressed after systemic therapy. These results suggest that BL-B01D1 could be a promising new agent for patients with la/mUC with few treatment options.	bladder
Sex and smoking bias in the selection of somatic mutations in human bladder.	Men are at higher risk of several cancer types than women(1). For bladder cancer the risk is four times higher for reasons that are not clear(2). Smoking is also a principal risk factor for several tumour types, including bladder cancer(3). As tumourigenesis is driven by somatic mutations, we wondered whether the landscape of clones in the normal bladder differs by sex and smoking history. Using ultradeep duplex DNA sequencing (approximately 5,000×), we identified thousands of clonal driver mutations in 16 genes across 79 normal bladder samples from 45 people. Men had significantly more truncating driver mutations in RBM10, CDKN1A and ARID1A than women, despite similar levels of non-protein-affecting mutations. This result indicates stronger positive selection on driver truncating mutations in these genes in the male urothelium. We also found activating TERT promoter mutations driving clonal expansions in the normal bladder that were associated strongly with age and smoking. These findings indicate that bladder cancer risk factors, such as sex and smoking, shape the clonal landscape of the normal urothelium. The high number of mutations identified by this approach offers a new strategy to study the functional effect of thousands of mutations in vivo-natural saturation mutagenesis-that can be extended to other human tissues.	bladder
Advancing Bladder Cancer Management: The Role of Neoadjuvant and Adjuvant Therapies and Biomarkers in Muscle Invasive Bladder Cancer.	The management of muscle-invasive bladder cancer (MIBC) is evolving rapidly, with the integration of neoadjuvant and adjuvant therapies and biomarker-driven patient selection now essential to refining treatment decisions. While cisplatin-based neoadjuvant chemotherapy has been the standard of care, its underutilization due to toxicity and patient ineligibility underscores the need for alternative strategies. Immune checkpoint inhibitors and targeted therapies, particularly fibroblast growth factor receptor (FGFR) inhibitors and antibody-drug conjugates (ADCs) like enfortumab vedotin (Nectin-4-directed) and disitamab vedotin (human epidermal growth factor receptor 2 [HER2]-directed), have transformed the management of metastatic urothelial carcinoma and are now being investigated in MIBC. The next challenge is to deploy these agents rationally by using robust biomarkers. FGFR3 alterations are predictive of response to FGFR inhibitors, whereas HER2 over-expression is chiefly prognostic but may also predict benefit from HER2-targeted ADCs. Circulating tumor DNA (ctDNA) is both prognostic and predictive, guiding dynamic therapy escalation when positive and potential de-escalation when negative in ongoing perioperative trials. In the adjuvant setting, immune-checkpoint blockade has begun to change practice: nivolumab in CheckMate 274 and pembrolizumab in the Alliance AMBASSADOR study each produced a statistically significant improvement in disease-free survival for high-risk patients after radical cystectomy, with overall survival (OS) data still Maturing. More recently, the phase 3 NIAGARA trial showed that adding perioperative durvalumab to neoadjuvant gemcitabine/cisplatin, followed by surgery and adjuvant durvalumab, conferred significant gains in both event-free survival and OS compared with chemotherapy alone. ctDNA's role as a marker of minimal residual disease is especially compelling. Trials, such as IMvigor010, have laid the foundation for ctDNA's utility as an MRD Marker, while the IMvigor 011 and VOLGA trials are utilizing ctDNA-driven treatment escalation or de-escalation to enable appropriate patient selection. Moving forward, the integration of multi-omics technologies, liquid biopsies, and adaptive trial designs will be crucial in optimizing treatment strategies. Challenges remain in standardizing biomarker assays, validating their predictive value, and translating findings into routine clinical practice. Collaborative efforts and large-scale prospective studies are necessary to bridge existing gaps and advance precision medicine tailored for MIBC.	bladder